In Europe the soil fumigant methyl bromide is still in use to control soil-borne diseases in greenhouses and open air vegetables. Methyl bromide is extremely toxic and environmental harmful. Countries under the Montreal protocol are demanded to reduce the use of methyl bromide with respect to the average use between 1991 and 1994 resulting in a total phase out from 2005 onwards for all applications except critical uses. For greenhouses replacement of soil grown crops by closed soilless growing systems has significant advantages: conservation of scarce water resources, no leaching of nutrients and pesticides and improved quality of products. A disadvantage of the closed system is the rapid dispersal of soil-borne pathogens by the recirculating nutrient solution. Disinfection of the nutrient solution either by active (sterilisation) or passive (part of the resident microflora survives the treatment) methods may eliminate harmful pathogens, but the hypothesis is that with passive methods a suppressive microflora can be built up, preventing (severe) outbreaks of certain pathogens. A 4-year EU-funded project had the aims to characterise the (suppressive) microflora and metabolites in the nutrient solution, to detect its dynamic behaviour during the cultivation of three crops (tomato, cucumber, gerbera) in a two year period and to demonstrate results to commercial users. Part of the crop was inoculated with Pythium aphanidermatum or Phytophthora cryptogea, while the nutrient solution was disinfected either with Ultra Violet radiation (active method) or slow sand filtration (passive method) or not at all (control). This paper emphasise on practical aspects of disinfection of the nutrient solution in relation to the presence and behaviour of the microflora. Results indicate that disinfection of the nutrient solution is needed to achieve proper yields. It was not proven that a suppressive microflora could be built up by a passive disinfection method, compared with active disinfection. However, a shift in the composition of the microflora could be detected, but the microflora in the stone wool growing system is mainly plant-driven, realising a microbial balanced system. Application of certain antagonists did also shift the total microflora during cropping, but did not suppress the mentioned pathogens with the exception of a Trichoderma-strain.